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  • In silico detection of SARS...
    Phan, Isabelle Q; Subramanian, Sandhya; Kim, David; Murphy, Michael; Pettie, Deleah; Carter, Lauren; Anishchenko, Ivan; Barrett, Lynn K; Craig, Justin; Tillery, Logan; Shek, Roger; Harrington, Whitney E; Koelle, David M; Wald, Anna; Veesler, David; King, Neil; Boonyaratanakornkit, Jim; Isoherranen, Nina; Greninger, Alexander L; Jerome, Keith R; Chu, Helen; Staker, Bart; Stewart, Lance; Myler, Peter J; Van Voorhis, Wesley C

    Scientific reports, 02/2021, Volume: 11, Issue: 1
    Journal Article

    Rapid generation of diagnostics is paramount to understand epidemiology and to control the spread of emerging infectious diseases such as COVID-19. Computational methods to predict serodiagnostic epitopes that are specific for the pathogen could help accelerate the development of new diagnostics. A systematic survey of 27 SARS-CoV-2 proteins was conducted to assess whether existing B-cell epitope prediction methods, combined with comprehensive mining of sequence databases and structural data, could predict whether a particular protein would be suitable for serodiagnosis. Nine of the predictions were validated with recombinant SARS-CoV-2 proteins in the ELISA format using plasma and sera from patients with SARS-CoV-2 infection, and a further 11 predictions were compared to the recent literature. Results appeared to be in agreement with 12 of the predictions, in disagreement with 3, while a further 5 were deemed inconclusive. We showed that two of our top five candidates, the N-terminal fragment of the nucleoprotein and the receptor-binding domain of the spike protein, have the highest sensitivity and specificity and signal-to-noise ratio for detecting COVID-19 sera/plasma by ELISA. Mixing the two antigens together for coating ELISA plates led to a sensitivity of 94% (N = 80 samples from persons with RT-PCR confirmed SARS-CoV-2 infection), and a specificity of 97.2% (N = 106 control samples).